As others have said, it's the WatchOn app. Took me a little while to figure out as well. The "remote" side of things is quite limited, so I'm not sure I'll actually use it, but it's a neat little app. I got mine set up with my TV, DVR Box, and Home Theater Receiver in no time. Just like setting up any universal remote, really. Strange it doesn't work with all IR components.
With that being said, the stuff you can do once everything is paired is sort of cool. It pulls up your local guide listings, tells you what's on, and gives you the option to watch/record it. I opened it up last night around 11, it told me I "might like" Conan, I hit record, and it immediately tuned my TV to 780 (TBS HD) and started recording.